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The rind phenotype of watermelon fruits is an important agronomic characteristic in the watermelon market. Inheritance and linkage analyses were performed for three rind-related traits that together determine the rind phenotype: foreground stripe pattern, rind background color, and depth of rind color. The inheritance of the foreground stripe pattern was analyzed using three different F₂ populations, showing that the striped pattern is dominant over the non-striped pattern. The inheritance analysis of the rind background color was performed using F₂ populations of the ‘10909’ and ‘109905’, and the depth of rind color was analyzed using F₂ populations of the ‘90509’ and ‘109905’. Yellow color was found to be dominant over green color, and a deep color was dominant over the standard color. Linkage analysis of the three traits was conducted using three F₂ populations in which two traits were segregating. Each pair of traits was inherited independently, which demonstrated that the three traits are not linked. Therefore, we propose a three-locus model for the determination of rind phenotype, providing novel insight that rind phenotype is determined by the combination of three genetically independent loci.